This doc has Aud’s edits on intro, data, references, photos etc that need to be copy and pasted into the overall doc where the statistical changes were made

(had to make new rmarkdoc b/c was one commit ahead of master)

Pacific Giant Salamander Image Source: Gary Nafis1

Introduction

(! this syntax is SoOoO STALE, HALP ! (but the info is good))

Pacific Giant Salamanders,(Dicamptodon tenebrosus) are the largest terrestrial salamander in North America, growing up to 13 inches in total length 2. Pacific Giant Salamanders(PGS) populations range from northern California to the Canadian border, but are absent from the Olympic Peninsula. Thier habitats consist of wetlands such as permanent rivers, streams, creeks and pools of forests3. PGS populations may be affected by increases in pressures associated with logging such as habitat destruction and increased silt in the water due to upstream disturbances. This report analyses the differences in PGS populations between old growth(OG) forests and clear cut (CC) forests located in the H.J. Andrews Experimental Forest near Blue River, Oregon.

Map Source: Oregon State University4

Data and Methods

The data5 analyzed for this report was collected from Mack Creek in the H.J. Andrews Experimental Forest in Oregon. Cuttthroat trout (Onchorhyncus clarki clarki) populations have been monitored since 1987 then monitoring of Pacific Giant Salamanders began in 1993. H.J. Andrews Experimental Forest contains two sections of clearcut forest (cleared in 1963) and an upstream 500 year old coniferous forest5. These two sections will be referred to as “clear cut”(CC) and “old growth”(OG) throughout this report.

Specimen were sampled via electro-fishing and captured vertebrates were measured and weighed. This report uses the salamander data regarding section (old growth or clearcut), channel-specification (cascades, pool or side-channel), salamander weight (grams), and the total salamander counts observed(n).

Salamander abundance across locations was explored using statistical tests including a chi-squared test, two-sample t-test, Cohen’s d, Levene’s test, one-way ANOVA, and Tukey’s test.

Results

Results A:

Describe the trends in graph (in text).

Figure 1 shows the overall trend of PGS population counts being lower in clear-cut ares when compared to counts from old-growth forest. The annual change, growth or declines, of the two populations follows the same trend. Between the years 2011 and 2014 there was an obvious decline in population of both sections. This decline in population may be due to….

Results B:

really rough analysis: Table 1 shows that in both clear-cut and old-growth sections, salamanders are primarily located in channels classified as cascades(over 60% relative abundance), followed by side-channels then the least amount of salamanders were found in pools. Total annual counts of each populaiton show that more salamanders were found in the clear-cut section of the forest.

Table 1 [displays] the 2017 salamander counts in each section and the relative proportions of salamanders in each channel classification(cascade, pool or side-channel)
Section Cascades Pool Side-channel
CC 247 (67%) 31 (8%) 90 (24%)
OG 201 (63%) 45 (14%) 74 (23%)

Results C:

Question: Is there a significant difference in where in the channel PGS are located between the two sections?

  • Report in text (in context of actual counts), referencing table from Part B

Forest section (clear cut or old growth) does not have a significant effect on salamander location (cascades, pool, or side channel) (\(\chi\)2(2) = 5.54, p = 0.06).

Results D:

Question: Is there a significant difference in mean weights for Pacific giant salamanders observed in the two forest sections (clear cut and old growth) in 2017?

Answer: In 2017…

  • There is not a significant difference in mean weights for Pacific giant salamanders observed in the two forest sections (clear cut and old growth).
  • There IS a significant difference in median weights for PGS between the two forest sections.

The two sections of forest in 2017 have overall salamander counts that differ by only 40 individual specimen. Pacific Giant Salamander mean wieght is 0.66 grams highers in clear cut forest sections than in old growth sections (5.43 and 4.77 grams, respectively).

  • mean weight of DITE in clear cut forest sections is 0.66 grams higher than in old growth sections (5.43 and 4.77 respectively).
  • similar counts in the two forest sections: 368 at CC, 328 at OG (40 indiv diff).
section median_weight mean_weight sdev count
CC 5.43 7.78 9.90 368
OG 4.87 6.70 9.04 320

Mean salamander weights for clear cut (7.78) and old growth (6.7) forest sections do not differ significantly (t(683.21) = (1.49, p = (0.138).

Results E:

Compare weights of Pacific giant salamanders in pools, cascades and side-channels of Mack Creek in 2017. Pool salamander observations from both the old growth and clear cut sections for this part (i.e., you will not consider “section” as a factor here).

First, visually compare Pacific giant salamander weights between the three channel classifications. You can choose how to best visualize the weights between the three groups (Beeswarm? Jitter? Histogram? Density? Something else?), but you should indicate values for the mean, and standard deviation, standard error or a 95% confidence interval. Add a figure caption.

Second, answer: Is there a significant difference in mean weights for Pacific giant salamanders observed in pools vs. cascades vs. side-channels in 2017? Describe the results of your statistical analysis in text, within the context of broader (and more important) measures of differences between groups (some options: means differences, effect sizes, percent differences, etc).

unittype mean_weight sd_weight sample_size se_weight var_weight
C 7.520850 9.027747 448 0.4265209 81.50021
P 9.297500 13.622957 76 1.5626603 185.58494
SC 5.676646 8.265256 164 0.6454081 68.31446

Third, describe any concerns you have about comparing means across the groups. What might be another option to consider moving forward with the analysis? (You don’t need to actually do that here, just describe briefly in 1-2 sentences.) - Using means to compare groupd lead to skewed data, as seen in Figure 2, there were many outliers in the weights of salamanders within each channel section. For data that contains outliers, comparing medians elimanates the skew and allows for more [equal, levelized, ] comparison among groups. “Panulirus interruptus; California Spiny Lobster.” CalPhotos, University of California, Berkeley, 1999, https://calphotos.berkeley.edu/cgi/img_query?enlarge=9092+3191+3541+0006

References

  1. “Dicamptodon tenebrosus; Pacific Giant Salamander.” Gary Nafis, California Herps, http://www.californiaherps.com/salamanders/images/dtenebrosusfchu3086.jpg

  2. “Coastal Giant Salamander - Dicamptodon tenebrosus.” California Herps, 2019, http://www.californiaherps.com/salamanders/pages/d.tenebrosus.html

  3. “Coastal Giant Salamander - Dicamptodon tenebrosus.” IUCN Red List of Threatened Species, 2015, https://www.iucnredlist.org/species/59081/78906025#habitat-ecology

  4. “Andrews Forest Map” HJ Andrews Experimental Forest Long-Term Ecological Research, 2017, https://andrewsforest.oregonstate.edu/data/map

  5. Gregory S. V. 2016. Aquatic Vertebrate Population Study in Mack Creek, Andrews Experimental Forest, 1987 to present. Environmental Data Initiative. https://doi.org/10.6073/pasta/5de64af9c11579266ef20da2ff32f702. Dataset accessed 12/01/2019.